Is there are preferred way to add functionality to libbladeRF / NIOS with regards to the messages sent and received from the NIOS core?

I'd like to make the changes compatible with the architecture so they could possibly be merged back into the code base. Eventually I'll get the bladeRF running completely headless from the USB connection. Currently the system is put into reset when USB disconnects, so there are changes all over the place that would need to be made to support that (FX3 firmware places the FPGA logic into reset when a disconnect happens, among other things -- and the VHDL code isn't really set up to work when part/all of the system is in reset, even with not so minor tweaks it'll be a big change).

I saw the USR1 message type. This is basically what I'm currently using for my extra message types.